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amsession/Kmer-based-Subgenome-Mapping

Hybridization brings together chromosome sets from two or more distinct progenitor species. Genome duplication associated with hybridization, or allopolyploidy, allows these chromosome sets to persist as distinct subgenomes during subsequent meioses. Here, we present a general method for identifying the subgenomes of a polyploid based on shared ancestry as revealed by the genomic distribution of repetitive elements that were active in the progenitors. This subgenome-enriched transposable element signal is intrinsic to the polyploid, allowing broader applicability than other approaches that depend on the availability of sequenced diploid relatives. We develop the statistical basis of the method, demonstrate its applicability in the well-studied cases of tobacco, cotton, and Brassica napus, and apply it to several cases: allotetraploid cyprinids, allohexaploid false flax, and allooctoploid strawberry. These analyses provide insight into the origins of these polyploids, revise the subgenome identities of strawberry, and provide perspective on subgenome dominance in higher polyploids.

Session, Adam↗

Guideline 36 Conformance Test v2.0

ASHRAE Guideline 36 provides guidance for how typical commercial building HVAC systems should be controlled to reduce energy costs and improve the indoor environmental quality for occupants. An industry-led effort is developing test scripts for how control manufacturers can test that the control logic in their control products follows Guideline 36. This software intends to support that effort in two ways. First, by providing a testbed for control manufacturers to run the test scripts against their own control products and compare their generated results to the expected results provided by the test scripts. Second, by providing a testbed that can be used during the development of test scripts to rapidly and repeatably verify they exercise Guideline 36 logic as desired and generate accurate expected results that control products can be compared to. An initial version of the software has already been developed and released open-source by a previous CEC-funded project that implemented the first use case (https://github.com/LBNL-ETA/guideline36_conformance_test/blob/master/LICENSE.txt), while this software disclosure will add the functionality of the second use case, as well as update the software where needed, all open-source. We intend to extend and contribute to the existing open-source software repository.

Blum, David [Lawrence Berkeley National Laboratory↗

Introduction to this special section: Geothermal energy

Geothermal energy is a global renewable resource that has the potential to provide a significant portion of baseload energy in many regions. In the United States, it has the potential to provide 8.5% of the electric generation capacity by the middle of the century. In general, geothermal systems require heat, permeability, and water to be viable for energy generation. However, with current technologies, only heat is strictly necessary in a native system. Engineered geothermal systems (EGS) introduce water into the subsurface at elevated pressures and reduced temperatures and enhance permeability through hydraulic and/or shear fracturing. Additionally, although moderate- to high-temperature resources currently dominate geothermal energy production, low-temperature resources have been utilized for direct-use cases. When well balanced and maintained, geothermal resources can produce significant amounts of heat and achieve long-term sustainability on the order of an estimated tens to hundreds of years.

15 GEOTHERMAL ENERGY↗

Initial development and verification of a primary load design method based on elastic-perfectly plastic analysis

This report describes a new primary load design method to supplement the current design-by-elastic-analysis rules in Section III, Division 5, Subsection HB, Subpart B of the ASME Boiler and Pressure Vessel Code, covering the design and construction of Class A high temperature nuclear structural components. The main objectives for the new design method are to provide a procedure that can be applied to components with complicated geometries and to simplify the primary load design process by providing rules more compatible with modern finite element analysis. The report includes a complete set of design rules, presented as a draft ASME Code Case, as well as a commentary on the rules and a set of verification problems. The verification design problems demonstrate the new primary load design rules produce safe, efficient components when compared to the current Division 5 approach, while greatly simplifying the design analysis process.

42 ENGINEERING↗

Collaborative Research: Explosive reconnection in relativistic magnetically-dominated plasmas (Final Report)

Magnetic fields can be the dominant component of astrophysical plasmas, so that the magnetic energy density might exceed even the rest-mass energy density of matter. In this extreme (and largely unexplored) regime the magnetic field controls the overall plasma evolution, dissipation, and acceleration of non-thermal particles. This plasma regime, applicable to a variety of astrophysical sources - magnetars, pulsars and pulsar wind nebulae (PWNe), jets of Active Galactic Nuclei (AGNs) and Gamma-Ray Bursters (GRBs) - is dramatically different from laboratory plasmas, the magnetospheres of planets, and the interplanetary plasma. Relativistic astrophysical sources then provide an unique opportunity to study the fundamental plasma physics of magnetically-dominated plasmas; a novel and fast-evolving field of theoretical research which, by investigating energy conversion and particle energization processes in plasmas, is of vital importance to the Fusion Energy Sciences DoE program. Data coming from astrophysical high-energy missions, especially the Crab Nebula flares recently observed by the Fermi and AGILE satellites, suggest that the acceleration of non-thermal particles to the highest energies occurs in magnetic reconnection events - a major change of paradigm in high-energy astrophysics. Most importantly, observations demand that particle acceleration should proceed extremely fast (with accelerating electric field of the order of the magnetic field) and on macroscopic scales (much larger, e.g., than the microscopic plasma skin depth). We are conducting studies of the microphysics of magnetically-dominated plasmas focussing in particular on the highly dynamic regime of explosive reconnection and associated particle acceleration in relativistic plasmas. We are studying the stability and explosive plasma dynamics, particle acceleration and radiation production in a number of idealized plasma configurations that approximate relevant astrophysical sources (like the magnetic ABC structures and interacting flux tubes, as well as generalizations of analytical models of X-point collapse to relativistic plasmas). The well-studied case of the Crab Nebula is taken as a prototypical example for the application of the model. We are combining analytical studies of explosive magnetic dynamics and dissipation in relativistic plasmas with particle-in-cell (PIC) simulations and fluid simulations. The theoretical model, fluid and particle-in-cell simulations are cross-checked for agreement and convergence.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DSO+T: Valuation Methodology and Economic Metrics (DSO+T Study: Volume 4)

This report summarizes a rigorous valuation analysis methodology used by the Distribution System Operator with Transactive (DSO+T) study to estimate the financial benefits and costs of adopting Transactive Energy coordination of distributed energy resources for key stakeholders (for example distribution system operators and customers). This was achieved by modeling the value exchanges between stakeholders and determining the annualized costs and revenues experienced by stakeholders, enabling the evaluation of overall impact on stakeholder’s annualized cash flow. Extensive work was conducted developing methods to estimate the operating costs of distribution system operators at a level of granularity that would allow the financial impact of implementing a transactive energy approach to be estimated. This work included developing parametric models for labor and software costs, distribution system capital and maintenance costs, growth rates, and factors to determine annualized costs of capital investments. Simulation results were used to calculate wholesale energy costs and revenues from retail sales. Valuation analysis methods were also developed for other stakeholders including customers, the transmission system operator, independent system operator, and generators. The resulting capability allows a complete mapping of the flow of financial value between stakeholders that can be directly integrated with the results of demand flexibility simulations. Example results are provided for a business-as-usual case and compared to a transactive energy case as well as to actual cost data.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Analysis of Approximations in Modeling of BWR Bundle Void Distributions

In boiling water reactors, complex heterogeneous bundle designs, control blades adjacent to the corner of bundles, and the presence of boiling can lead to complex internal void distributions. A few approximations exist to model these void distributions. They could be modeled using a 1D axial solver in which each axial node is assumed to be at an average void, or each pin cell could be modeled with its own void concentration. In the latter case, the void could be discretized in pin-centered or coolant-centered channels. The goal of this project was to quantify the effect of using the different approximations for modeling internal void distributions on neutronics calculations. Using 3D void distributions calculated with CTF, Monte Carlo Neutral Particle (MCNP) transport code models were created for GE-9 and GE-14 lattices. For each model, the internal void distribution from CTF at a given axial node was selected, and a lattice calculation was carried out with MCNP. Comparisons between models using a lattice-averaged void, or using a void distribution in coolant-centered channels, showed large differences in reactivity which in some cases were well above 1,000 pcm, and it also showed differences in normalized fission rates greater than 20%. It was also found that using a lattice average void can lead to a significant difference in the estimation of the worth of a control blade. The differences found when comparing results from models using pin-centered and coolant-centered channels were up to 200 pcm in reactivity and up to 1.4% in the normalized fission rates. In addition to these two sets of comparisons, MCNP models were set up so that each subchannel had a saturated liquid component around the fuel pins and a saturated vapor component in the center to approximate annular flow. In comparison to the models using coolant-centered subchannels, up to 1–3% differences in normalized fission rates could be found.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Status of the Ce+BAF project

Jefferson Lab is proposing to add positron beams to the 12 GeV Continuous Electron Beam Accelerator Facility (CEBAF). A team of accelerator and nuclear scientists was formed in 2018 to develop the physics case as well as a concept for the generation, production and delivery of Continuous (CW) polarized positron beams to the experimental halls, up to the full 12 GeV. A layout of the proposed concept will be shown. We will report on the ongoing efforts in the positron generation and capture, target design, beam transport and expected properties of the e+ beam on the experimental targets at 12GeV. This project is supported by the U.S. Department of Energy, Office of Science, Office of Nuclear Physics under contract DE-AC05-06OR23177

Roblin, Yves↗

Summary of Potential Incidents and Consequences from Carbon Dioxide Pipeline and Storage Systems Construction and Operation

This document provides a high-level summary of the potential human and environmental impacts associated with carbon dioxide (CO 2 ) pipeline transport, injection, and storage activities. It also reviews lessons learned from natural and industrial analogs of CO 2 storage as well as case studies of notable accidental CO 2 releases. The analysis is structured into several key sections, each addressing specific resource impacts and potential consequences.

54 ENVIRONMENTAL SCIENCES↗

HydroMINE: Simple, Modular and Scalable (Final Scientific/Technical Report)

Hydromine is a novel extremely versatile solution to hydrokinetics energy generation, where the external water flow facing energy sweeping area (&structure) is completely passive. One or multiple Hydromine units can easily deploy from a multitude of floating or stationary marine structures, opening a multitude of application and use cases. Proposing Hydromine, it was initially found that the concept could easily scale into all of the four areas of ARPA-E SHARKS cases, as well as other applications, this is illustrated in Figure 1. Also, the relatively aggressive cost of energy targets of the program could be met in the conceptual phase.

13 HYDRO ENERGY↗

Review of the 1st EUV Light Sources Code Comparison Workshop

We review the results of the 1 st Extreme Ultraviolet (EUV) Light Sources Code Comparison Workshop. The goal of this workshop was to provide a platform for specialists in EUV light source plasma modeling to benchmark and validate their numerical codes using well-defined case studies. Detailed consideration of a plethora of atomic collisional and radiative processes is required for modeling EUV light source plasmas. Eight institutions spanning four countries contributed data to the workshop. Two topics were addressed, namely (i) the atomic kinetics and radiative properties of tin plasmas under EUV-generating conditions and (ii) laser absorption in a fully ionized, one-dimensional hydrogen plasma. In this paper, we summarize the key findings of the workshop and outline plans for future iterations of the code comparison activity.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NOvA 2024 official data release (26.61E20 neutrino + 12.5E20 antineutrino)

This data release corresponds to the Bayesian 2024 analysis of NOvA $\nu_e$ appearance and $\nu_{\mu}$ disappearance data, corresponding to analysis described in https://arxiv.org/abs/2509.04361. File `NOvA_2024_data_histograms.root` contains data histograms for all the NOvA data samples. Exposure: * neutrino-enhanced beam: 26.61E20 protons on target * antineutrino-enhanced beam: 12.5E20 protons on target External constraints: * ss2th12=0.851, dm21=7.53e-5 are fixed at 2019 PDG values, with negligible effect on NOvA predictions. * ss2th13 & dm32: * RCDB1D: 1D constraint from Daya Bay for ss2th13, 0.0851+/-0.0024 * RCDB2D: Correlated 2D constraint from Daya Bay on ss2th13 & dm32, available in their official 2023 data release: https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.130.161802#supplemental An additional file containing the predictions (`NOvA_2024_prediction_with_systs_histograms.root`) for all channels’ signal and background components computed at the NOvA best-fit oscillation parameters and systematic pull terms. Numu samples include the no-oscillation case as well. Please note that any fits performed with these histograms are not expected to exactly reproduce the official NOvA results as parameterizations of the numerous systematic uncertainties considered in the official fits are not included in this release. The zip file also contains the 2D credible interval contours, with details in a README.md

Sztuc, Artur [University Coll. London] (ORCID:0000↗

Moving Zero Energy Office Buildings to the Mainstream: Establishing Design Guidelines and Energy Targets: Preprint

Office buildings represent a significant portion of the commercial sector and are ideal candidates to lead the market towards achieving zero energy or zero energy ready buildings. The variety of sizes and uses for office buildings make them challenging to determine set design guidance that can be deployed across the market. A project committee for ASHRAE’s Zero Energy - Advanced Energy Design Guide (ZE-AEDG) for small and medium office buildings , comprised of members from five major national associations with market-pull in commercial buildings, created design guidance for achieving zero energy office buildings for new construction and major retrofit. This design guidance focuses on the process, providing a pathway for both office owners and design teams to achieve zero energy status. Energy use intensity targets range from 16 kBtu/ft²·yr to 36 kBtu/ft²·yr for the different climate zones were established such that office buildings can be “zero-ready,” that is, having low energy consumption that can easily be offset with renewables, preferably on-site. The design guidance was rooted in extensive energy modeling, as well as case studies of actual office buildings that have achieved high levels of energy performance and met zero energy or zero energy ready status. A unique aspect of the zero-energy guide is that it is not compared against a baseline but focuses on achieving an absolute target. The paper presents process of creating the targets, the selection of strategies to achieve the targets, and sample case studies that show how the cost-sensitive solutions are achievable for the design community. It also presents outreach strategies to deploy market achievable zero energy measures.

buildings↗

Status of the Ce+BAF project

Jefferson Lab is proposing to add positron beams to the 12 GeV Continuous Electron Beam Accelerator Facility (CEBAF). A team of accelerator and nuclear scientists was formed in 2018 to develop the physics case as well as a concept for the generation, production and delivery of Continuous (CW) polarized positron beams to the experimental halls, up to the full 12 GeV. A layout of the proposed concept will be shown. We will report on the ongoing efforts in the positron generation and capture, target design, beam transport and expected properties of the e+ beam on the experimental targets at 12GeV. This project is supported by the U.S. Department of Energy, Office of Science, Office of Nuclear Physics under contract DE-AC05-06OR23177

Roblin, Yves↗

TCF - Sustainable Well Cement for Geothermal, Thermal Recovery, and Carbon Storage wells

Primary cementing is the most important operation performed on a subterranean well. Cement, placed in the annulus between the casing and the formations, serves as a hydraulic seal preventing fluids and gas migrations, protecting steel casing from corrosion, and supporting the well structure. Poor cementing jobs can be directly responsible for wells not reaching their full capacity, casing corrosion, compromised well integrity and, in the worst-case scenarios, well collapse. Geothermal, thermal recovery, and carbon storage wells offer environments that are especially difficult for cements to survive while the required lifespan of these wells can be years. In these wells currently used cements cannot provide durable well integrity, and new solutions are necessary. The necessity of stabilizing the electric grid, increasing its flexibility, and providing energy on demand will further expand the market of durable cement solutions for applications in high-temperature underground reservoir thermal energy storage wells (HT RTES). The design challenges of special cement systems for such wells originate from chemistry limitations of currently used well cements, aggressive environments, temperature and repeated shock conditions associated with them, and very weak formations that are not uncommon in these wells. During the last 70 years the most common systems for thermal-well construction have been Ordinary Portland Cement (OPC) (absolute majority of the wells), silica-lime system, and high aluminum cement-containing formulations. The major issues of calcium-silicate hydrates, that form during the hydration of OPC resulting in hardened material, are their poor chemical resistance to acids due to the calcium interactions with acid anions followed by its eventual dissolution, even in mild acids, such as carbonic acid from CO 2 dissolution, and inadequate bonding to the steel causing serious casing corrosion problems (Sugama & Pyatina, 2019). Performance of OPC-based cement may be significantly improved with organic additives; however, those are limited by their temperature stability. An alternative to calcium-silicate cement was developed by BNL and commercialized by Halliburton as ThermaLock TM cement. Calcium-aluminate-phosphate-based chemistry of the material allowed overcoming acid-resistance problems of OPC, especially in CO 2 -rich geothermal environments. In 2012-2015, building upon this experience, BNL developed Thermal Shock Resistant Cement (TSRC) with the support of Geothermal Technology Office (GTO) of DOE. TSRC has high-temperature stable chemistry, superior properties of cement-metal casing bond and corrosion protection (4-times better than currently used OPC-based formulation), significantly outperforms common well-cements in thermal-shock tests, has self-healing properties, and like ThermaLock TM is CO 2 resistant incorporating carbonate ions into stable hydrates (Gill et al., 2012).

15 GEOTHERMAL ENERGY↗

Machine learning based rate optimization under geologic uncertainty

We propose a novel approach for rate optimization during a waterflood under geologic uncertainty in reservoir properties such as permeability and porosity. The traditional approach typically involves several runs of the forward simulator. This may not scale well when the optimization is to be performed at the full field-level and over multiple geologic realizations. A machine-learning (ML) based approach which is quick and scalable for rate optimization over multiple geologic realizations is proposed instead. The training data for the model is generated by running the forward simulator with randomly assigned well rates using multiple geologic realizations. A reduced order representation of the permeability heterogeneity in each of the realizations is derived using a grid connectivity transformation (GCT). This step involves finding basis functions corresponding to the different modal frequencies of the grid connectivity represented by the grid Laplacian. The projection of the heterogeneous property field along these basis functions gives the basis coefficients that form the reduced order representation. Subsequently, for each training datapoint, streamlines are traced and the minimum time of flight (TOF) representing the tracer breakthrough time at each producer is recorded. The basis coefficients and well rates are fed to a machine learning model as input and the minimum TOF at the producers forms the output of the model. This trained model can then be used along with an optimizer for computing the optimal injection rates to maximize the injection sweep efficiency. This corresponds to minimizing the variance in the minimum TOF within each well group. Different architectures of neural network are tested using 5-fold cross validation to decide the best ML model to compute the streamline time of flight. The trained model is used to perform well rate optimization over multiple realizations of geology by using a risk tolerance penalty. The optimal well rates thus obtained are compared with two cases: a) equal well rates assigned to all injectors and producers and b) well rates obtained by optimizing over a single realization without considering the uncertainty in geology. The optimal well rates are seen to offer better oil recovery and sweep efficiency than both cases.

02 PETROLEUM↗

Shear strength and permeability of the cement-casing interface

Here, the shear strength and hydraulic permeability of the interface between well cement and casing was investigated using a triaxial direct shear apparatus. For the first time, these experiments provide measurements under controlled stress conditions with fluid flow measurements along the interface. The low cohesion (1.1 ± 1.1 MPa) and the high friction angle (43.4 ± 2.0°) indicates that the shear strength of the interface is provided by friction. This implies that the state of stress of the cement is critical to well integrity. The hydraulic aperture of the undamaged cement-steel samples was 6.8 ± 1.0 microns. Shear damage to the interface caused a decrease (-20 %) in hydraulic aperture for samples aged up to 1 month, and an increase (+300 %) for samples cured for two years. We performed numerical simulations to estimate the leakage potential from a carbon storage operation. This model predicts negligible leakage amounts (47 tonnes) in a shear-damaged well for the modeled injection of ~1.26 million tonnes of CO 2 . Thus, our measurements indicate that the cement-casing interface is not a significant leakage pathway in its intact or damaged state, and that shear-driven failure scenarios for this interface are not a significant risk to CO 2 storage security.

54 ENVIRONMENTAL SCIENCES↗